LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-106-g5d02e140d4)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
  using 1 OpenMP thread(s) per MPI task
# flat membrane demo
variable     r0 equal  0.97
variable     d1 equal  ${r0}
variable     d1 equal  0.97
variable     d2 equal  sqrt(3.0)*${r0}
variable     d2 equal  sqrt(3.0)*0.97
variable     d3 equal  3.0*${r0}
variable     d3 equal  3.0*0.97
variable     ro equal  2./${d1}/${d2}/${d3}
variable     ro equal  2./0.97/${d2}/${d3}
variable     ro equal  2./0.97/1.68008928334181/${d3}
variable     ro equal  2./0.97/1.68008928334181/2.91

variable     T  equal  0.23
variable     LD equal  1.0

units        lj
atom_style   ellipsoid

boundary     p p p

lattice      custom ${ro} a1 ${d1}  0.0 0.0 a2 0.0 ${d2}  0.0              a3 0.0 0.0 ${d3}  basis 0.0 0.0 0.0 basis 0.5  0.5  0.0
lattice      custom 0.421728460751825 a1 ${d1}  0.0 0.0 a2 0.0 ${d2}  0.0              a3 0.0 0.0 ${d3}  basis 0.0 0.0 0.0 basis 0.5  0.5  0.0
lattice      custom 0.421728460751825 a1 0.97  0.0 0.0 a2 0.0 ${d2}  0.0              a3 0.0 0.0 ${d3}  basis 0.0 0.0 0.0 basis 0.5  0.5  0.0
lattice      custom 0.421728460751825 a1 0.97  0.0 0.0 a2 0.0 1.68008928334181  0.0              a3 0.0 0.0 ${d3}  basis 0.0 0.0 0.0 basis 0.5  0.5  0.0
lattice      custom 0.421728460751825 a1 0.97  0.0 0.0 a2 0.0 1.68008928334181  0.0              a3 0.0 0.0 2.91  basis 0.0 0.0 0.0 basis 0.5  0.5  0.0
Lattice spacing in x,y,z = 0.97 1.6800893 2.91


region       box block   0 40  0 24  -20  20
create_box   1 box
Created orthogonal box = (0 0 -58.2) to (38.8 40.322143 58.2)
  1 by 1 by 4 MPI processor grid
region       membrane block  0 40  0 24 -0.5 0.5
create_atoms 1 region membrane
Created 1920 atoms
  using lattice units in orthogonal box = (0 0 -58.2) to (38.8 40.322143 58.2)
  create_atoms CPU = 0.001 seconds

group        membrane  region membrane
1920 atoms in group membrane

set type 1 mass  1.0
Setting atom values ...
  1920 settings made for mass

set type 1 shape  1 0.99 0.99
Setting atom values ...
  1920 settings made for shape

set          group all quat 0 -1 0  90
Setting atom values ...
  1920 settings made for quat

#compute      memb  all temp/com
#compute      rot all temp/asphere bias memb
velocity     all create ${T} 87287 loop geom
velocity     all create 0.23 87287 loop geom

pair_style   ylz  2.6
pair_coeff   *  *   1.0  1.0  4  3  0.0  2.6
neighbor     1.0 bin


thermo_style custom step temp press pxx pyy
thermo       200

timestep     0.01

#dump         1 all atom 10 dump_onlymembrane.lammpstrj

fix          1 all langevin ${T} ${T}  ${LD}  48279
fix          1 all langevin 0.23 ${T}  ${LD}  48279
fix          1 all langevin 0.23 0.23  ${LD}  48279
fix          1 all langevin 0.23 0.23  1  48279


fix          2 all nve/asphere
run          3000

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- pair ylz command:

@Article{Yuan10,
 author =  {H. Yuan, C. Huang, J. Li, G. Lykotrafitis, and S. Zhang},
 title =   {One-particle-thick, solvent-free, coarse-grained model for biological and biomimetic fluid membranes},
 journal = {Phys. Rev. E},
 year =    2010,
 volume =  82,
 pages =   {011905}
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 3.6
  ghost atom cutoff = 3.6
  binsize = 1.8, bins = 22 23 65
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair ylz, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.182 | 4.794 | 5.472 Mbytes
   Step          Temp          Press           Pxx            Pyy      
         0   0.23          -0.0073508785  -0.012283389   -0.012234574  
       200   0.21866566    -0.0011213114  -0.0017540296  -0.0017008786 
       400   0.22409469    -0.00055137604 -0.00050366017 -0.0012846672 
       600   0.21623646    -0.0004808564  -0.00063496522 -0.00071617302
       800   0.22248339    -0.00066333806 -0.00093812145 -0.00099410261
      1000   0.22367907    -0.0003439459  -0.00076259578 -0.00013354375
      1200   0.23276206     8.5764334e-06 -0.00036165178  0.00038543803
      1400   0.23129049    -5.1997966e-06 -0.00040514787  0.00017093646
      1600   0.22074564    -0.0001604642  -0.00053959031  9.0463391e-05
      1800   0.2276062     -0.00015655254 -0.00042925633  5.4938379e-05
      2000   0.22469391    -3.6198836e-05 -1.8538296e-06 -0.00010464749
      2200   0.22737515    -1.8967356e-05  0.0001341006  -0.00022739894
      2400   0.22607533     0.00014650382 -2.4871789e-05  0.00058296255
      2600   0.24044743     0.00045066449  0.00049153595  0.00078042437
      2800   0.23346628     0.00017994019 -5.0897724e-05  0.00046011801
      3000   0.22427206     0.00040437022  0.00049580531  0.00046259202
Loop time of 5.04539 on 4 procs for 3000 steps with 1920 atoms

Performance: 513736.789 tau/day, 594.603 timesteps/s, 1.142 Matom-step/s
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 4.1163     | 4.2634     | 4.4004     |   6.5 | 84.50
Neigh   | 0.00088605 | 0.032793   | 0.083516   |  19.1 |  0.65
Comm    | 0.006704   | 0.20003    | 0.40672    |  42.5 |  3.96
Output  | 0.00033812 | 0.0012192  | 0.0020905  |   2.3 |  0.02
Modify  | 0.00035967 | 0.20167    | 0.42535    |  45.0 |  4.00
Other   |            | 0.3462     |            |       |  6.86

Nlocal:            480 ave        1052 max           0 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Nghost:          854.5 ave        1801 max           0 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Neighs:        11684.2 ave       31145 max           0 min
Histogram: 2 0 0 0 0 1 0 0 0 1

Total # of neighbors = 46737
Ave neighs/atom = 24.342188
Neighbor list builds = 98
Dangerous builds = 0


Total wall time: 0:00:05
